Biology subjects

Alenquer, M.

Publications and source records attributed to Alenquer, M..

9 recordsLinked to original sources

bioRxiv2026

Age-dependent disease tolerance to SARS-CoV-2 infection

Disease tolerance limits infectious disease severity through tissue damage control mechanisms that do not target pathogens directly. Here we demonstrate that age-dependent decline in adipose tissue lipolysis compromises disease tolerance to SARS-CoV-2 infection. Young adult mice exhibited robust adipocyte lipolysis and 80% survival, whereas old mice showed impaired adipocyte lipolysis and only 20% survival. Genetic repression of adipocyte lipolysis eliminated this age-dependent survival advantage without affecting viral titers, revealing that adipocyte lipolysis is essential for disease tolerance to SARS-CoV-2 in young adults. Impaired adipocyte lipolysis in aged mice was associated with a plasma lipidomic signature that predicts COVID-19 severity and mortality in three independent human cohorts. Mechanistically, adipocyte lipolysis provides free fatty acids (FFA) to support bone marrow emergency myelopoiesis, through CD36- and CPT1-dependent FFA cellular uptake and mitochondrial import, respectively. Bone marrow derived monocytes migrate to the lung via CCL2/CCR2-dependent mechanism where they enforce an immune-metabolic communication network with parenchymal cells to sustain lung structure and function. This circuit is not required to confer protection against influenza infection, revealing pathogen-specific disease tolerance mechanisms. These findings reveal adipose tissue catabolism as a central age-dependent factor responsible for exacerbated COVID-19 mortality in aged populations. One-Sentence SummarySARS-CoV-2 infection induces adipose tissue lipolysis to release fatty acids that drive myelopoiesis and monocyte production for lung protection and COVID-19 disease tolerance, but this protective circuit declines with age, increasing disease severity in the elderly.

immunology↗

bioRxiv2025

Functional redundancy in Oxa1-family insertases supports robust membrane insertion of influenza A virus M2 viroporin

The biogenesis of thousands of highly diverse membrane proteins in humans is facilitated by an array of ER-resident membrane protein translocases. While some membrane proteins have a strict requirement for a specific insertion machinery, membrane proteins with short translocated domains may be able to access multiple pathways. Here, we quantify the functional importance of redundancy in membrane protein translocation during influenza A virus (IAV) infection by examining the biogenesis of the viroporin M2. Given the wide host and cellular tropism of IAV, the virus likely evolved mechanisms to leverage host translocation pathways efficiently. We demonstrate that although M2 utilizes the ER membrane protein complex (EMC), driven by signals encoded in its transmembrane and C-terminal domains, M2 maintains an approximately 50% membrane insertion rate in the absence of the EMC. This influences viral cell-to-cell transmission across different IAV strains, with a greater impact on those expressing lower levels of M2. We identify alternative translocation of M2 via Oxa1-family translocons independent of canonical targeting chaperones. These findings reveal how the exploitation of multiple redundant pathways can ensure robust IAV infection. SIGNIFICANCE STATEMENTIAV must rapidly replicate in diverse mammalian hosts, which requires efficient integration of viral proteins into host cell membranes. This study uncovers how the viral proton channel M2 utilizes multiple redundant protein insertion pathways, accessing EMC and alternative Oxa1-family translocases. Revealing these redundant strategies clarifies how cells triage membrane proteins, offering insights into both viral adaptation and host cell robustness.

cell biology↗

bioRxiv2025

Membrane association prevents premature degradation and mitigates inefficient biogenesis of suboptimal membrane proteins

Accurate membrane protein biogenesis is essential for cellular function, yet many proteins contain suboptimal targeting or insertion signals. Influenza A virus (IAV) faces similar constraints during infection but may have evolved strategies to enhance the biogenesis of its own membrane proteins. One such protein, the viroporin M2, contains functionally essential hydrophilic residues within its transmembrane domain, which should hinder efficient membrane insertion. We hypothesize that IAV has adapted to overcome these sequence-based limitations and ensure robust M2 biogenesis. Using a biotin pulse-labelling system in intact cells, we uncover the dynamics of M2 targeting and ER insertion. Attenuating the insertion rate by ablating a key insertion factor, the ER membrane protein complex (EMC), leads to M2 accumulating in the cytosol, but remaining partially insertion competent. We find that cytosolic stability of non-inserted M2 is crucial for efficient biogenesis under these conditions and identify amphipathic helix- mediated membrane association as the molecular mechanism that counteracts proteasomal degradation. We propose membrane association as a novel buffering mechanism that regulates membrane protein biogenesis by stabilizing pre-insertion intermediates. SIGNIFICANCE STATEMENTMembrane proteins failing to insert into the endoplasmic reticulum (ER) may be rapidly degraded to avoid protein aggregation in the cytosol. Our findings challenge this prevailing view. We show that the influenza A viroporin M2, despite possessing unfavourable features for membrane insertion, can increase biogenesis efficiency by associating with the membrane prior to insertion. Membrane association buffers the protein against quality control pathways and promotes successful biogenesis--even in the absence of a key insertion factor. These results reveal an alternative fate for non-inserted membrane proteins and uncover a viral strategy that redefines how cells manage unstable insertion intermediates.

cell biology↗

bioRxiv2025

Bacteriocin-mediated prevention of secondary pneumococcal pneumonia by a human commensal Streptococcus mitis strain

Streptococcus pneumoniae remains a major public health threat despite widespread use of vaccines and antibiotics. Its well-established synergy with influenza A virus (IAV) often results in secondary bacterial pneumonia, a condition associated with high morbidity and mortality. As pneumococcal pneumonia is invariably preceded by nasopharyngeal colonization, preventing colonization represents a promising intervention strategy. Current approaches, including pneumococcal conjugate vaccines and antibiotics, can drive serotype replacement and antimicrobial resistance, underscoring the need for novel, targeted, and serotype-independent alternatives. We previously identified seven commensal streptococcal strains (S. oralis A22 and S. mitis B22-G22) that robustly inhibit S. pneumoniae growth and biofilm formation in vitro. Here, using a murine model, we demonstrate that colonization with the commensal strain F22Ad significantly reduces pneumococcal density in the nasopharynx by day 10 post-infection and prevents pneumococcal dissemination to the lungs following IAV co-infection. This protective effect was dependent on bacteriocins encoded at the blp1 locus. Among these, Bac2v1 (alone or in combination with Bac1) significantly reduced pneumococcal colonization. Notably, Bac2v1 exerted serotype-independent inhibitory activity, impairing the growth of diverse pneumococcal strains. Our findings provide the first in vivo proof-of-concept that commensal streptococci, and specifically their bacteriocins, can disrupt S. pneumoniae colonization and prevent progression to secondary bacterial pneumonia. This work introduces a previously unrecognized precision-based approach to pneumococcal disease prevention, offering a potential complement to current strategies.

microbiology↗

bioRxiv2025

A Metabolite-Based Resistance Mechanism Against Malaria

Whether jaundice, a common presentation of Plasmodium (P.) falciparum malaria (1-3) arising from the accumulation of circulating bilirubin, represents an adaptive or maladaptive response to Plasmodium spp. infection is not understood (1-3). We found that asymptomatic P. falciparum infection was associated with a >10-fold higher ratio of unconjugated bilirubin over parasite burden, compared to symptomatic malaria. Genetic suppression of bilirubin synthesis by biliverdin reductase A (BVRA) (4) increased parasite virulence and malaria mortality in mice. Accumulation of unconjugated bilirubin in plasma, via genetic inhibition of hepatic conjugation by UDP glucuronosyltransferase family 1 member A1 (UGT1A1) (5), was protective against malaria in mice. Unconjugated bilirubin inhibited P. falciparum proliferation in red blood cells (RBC) via a mechanism that suppressed mitochondrial pyrimidine synthesis. Moreover, unconjugated bilirubin inhibited hemozoin (Hz) crystallization and compromised the parasites food vacuole. In conclusion, jaundice represents a metabolic response to Plasmodium spp. infection that limits malaria severity.

immunology↗

bioRxiv2022

Influenza A virus liquid condensates can undergo pharmacological hardening

Multiple viral infections form biomolecular condensates in the host cell to compartmentalize viral reactions. Accumulating evidence indicates that these viral condensates may be hardened, a strategy with potential for exploitation as novel antiviral therapy, given that viral reactions rely on specific material properties for function. However, there is no molecular understanding on how to specifically and efficiently modify the material properties of viral condensates, a pre-requisite for overcoming off-target effects by rational drug design. In vitro, the material properties of biological condensates are modified by different thermodynamic parameters, including free energy, concentration, and type/strength of interactions. Here, we used influenza A virus liquid cytosolic condensates, A.K.A viral inclusions, to provide a proof of concept that modulating the type/strength of transient interactions among the interactome in IAV inclusions is more efficient at hardening these structures than varying the temperature or concentration, both in in vitro and in in vivo models. This stabilization can be achieved by a known pharmacological sticker that can specifically change the material properties of viral inclusions without affecting host proteome abundance nor solubility. Our work supports the development of antivirals targeting the material properties of biomolecular condensates in viral infections. It also provides a framework for the selection of compounds with this activity for general application and thus provides an advance in disease therapy.

cell biology↗

bioRxiv2021

Amino acids 484 and 494 of SARS-CoV-2 spike are hotspots of immune evasion affecting antibody but not ACE2 binding

Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike. Mutations in spike impacting antibody and/or ACE2 binding are appearing worldwide, with the effect of mutation synergy still incompletely understood. We engineered 25 spike-pseudotyped lentiviruses containing individual and combined mutations, and confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and N501Y. Our analysis of synergic mutations provides a landscape for hotspots for immune evasion and for targets for therapies, vaccines and diagnostics. One-Sentence SummaryAmino acids in SARS-CoV-2 spike protein implicated in immune evasion are biased for binding to neutralizing antibodies but dispensable for binding the host receptor angiotensin-converting enzyme

immunology↗

bioRxiv2019

Upstream translation initiation expands the coding capacity of segmented negative-strand RNA viruses

Segmented negative-strand RNA viruses (sNSVs) include the influenza viruses, the bunyaviruses, and other major pathogens of humans, other animals and plants. The genomes of these viruses are extremely short. In response to this severe genetic constraint, sNSVs use a variety of strategies to maximise their coding potential. Because the eukaryotic hosts parasitized by sNSVs can regulate gene expression through low levels of translation initiation upstream of their canonical open reading frames (ORFs), we asked whether sNSVs could use upstream translation initiation to expand their own genetic repertoires. Consistent with this hypothesis, we showed that influenza A viruses (IAVs) and bunyaviruses were capable of upstream translation initiation. Using a combination of reporter assays and viral infections, we found that upstream translation in IAVs can initiate in two unusual ways: through non-AUG initiation in virally encoded untranslated regions, and through the appropriation of an AUG-containing leader sequence from host mRNAs through viral cap-snatching, a process we termed start-snatching. Finally, while upstream translation of cellular genes is mainly regulatory, for sNSVs it also has the potential to create novel viral gene products. If in frame with a viral ORF, this creates N-extensions of canonical viral proteins. If not, it allows the expression of cryptic overlapping ORFs, which we found were highly conserved in IAV and widely distributed in peribunyaviruses. Thus, by exploiting their hosts capacity for upstream translation initiation, sNSVs can expand still further the coding potential of their extremely compact RNA genomes.

molecular biology↗

bioRxiv2018

INFLUENZA A VIRUS RIBONUCLEOPROTEINS FORM LIQUID ORGANELLES AT ENDOPLASMIC RETICULUM EXIT SITES

Influenza A virus has an eight-partite RNA genome that during viral assembly forms a supramolecular complex containing one copy of each RNA. Genome assembly is a selective process driven by RNA-RNA interactions and is thought to lead to discrete punctate structures scattered through the cytosol. Here, we show that contrary to the accepted view, formation of these structures is not dependent on RNA-RNA interactions among distinct viral ribonucleoproteins (vRNPs), as they assemble in cells expressing only one vRNP type. We demonstrate that these viral inclusions display characteristics of liquid organelles, segregating from the cytosol without a delimitating membrane, dynamically exchanging material, deforming easily and adapting fast to hypotonic shock. We provide evidence that they develop close to the Endoplasmic Reticulum Exit Sites (ERES), being dependent on continuous ER-Golgi vesicular cycling. We show that viral inclusions do not promote escape to interferon response, and propose that they facilitate selected RNA-RNA interactions in a liquid environment of concentrated vRNPs.

microbiology↗